The two leaders "shared their perspectives" on the situation in Syria and expressed their "strong concerns" about the impact of the conflict on the region.
Obama stressed his administration's "continued commitment" to provide support to the Syrian opposition coalition and the supreme military council, Xinhua cited the White House as saying in a statement.
The president last month authorised the shipment of small arms and ammunition to Syrian rebels in a stepped-up effort to support the opposition. Saudi Arabia has also been an arms supplier to the rebels.
On the situation in Egypt, the two leaders agreed that their countries have a "shared interest" in supporting Egypt's stability.
"The president expressed his serious concern about the violence in Egypt and underscored the urgent need for an inclusive political process that will enable an early return to a democratically elected civilian government in Egypt," the White House statement said.
Earlier this month, the Egyptian military removed president Mohamed Morsi from power on the grounds that he had failed to rein in mass protests against his "poor performance" and "maladministration".
The Obama administration has not defined the move as a coup, enabling it to continue its $1.55 billion annual aid.
Saudi Arabia has also pledged $5 billion in grants and loans to Egypt's interim government.
Meanwhile, the US State Department Friday echoed an appeal made by the German foreign ministry for the release of Morsi, who has been detained following his ouster.